High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities

Abstract

Viruses in the order Picornavirales infect eukaryotes, and are widely distributed in coastal waters. Amplicon deep-sequencing of the RNA dependent RNA polymerase (RdRp) revealed diverse and highly uneven communities of picorna-like viruses in the coastal waters of British Columbia (BC), Canada. Almost 300 000 pyrosequence reads revealed 145 operational taxonomic units (OTUs) based on 95% sequence similarity at the amino-acid level. Each sample had between 24 and 71 OTUs and there was little overlap among samples. Phylogenetic analysis revealed that some clades of OTUs were only found at one site; whereas, other clades included OTUs from all sites. Since most of these OTUs are likely from viruses that infect eukaryotic phytoplankton, and viral isolates infecting phytoplankton are strain-specific; each OTU probably arose from the lysis of a specific phytoplankton taxon. Moreover, the patchiness in OTU distribution, and the high turnover of viruses in the mixed layer, implies continuous infection and lysis by RNA viruses of a diverse array of eukaryotic phytoplankton taxa. Hence, these viruses are likely important elements structuring the phytoplankton community, and play a significant role in nutrient cycling and energy transfer.

Keywords: Picornavirales; RNA viruses; phytoplankton mortality; pyrosequencing; viral diversity; viral ecology.

Figure 1

Location of sampling sites. Map showing the location of sampling sites within the Strait of Georgia (SOG) and Jericho Pier, adjacent to Vancouver, British Columbia, Canada. Jericho Pier was sampled in summer (JP-S) and fall (JP-F).

Figure 2

Environmental parameters. (A) Chlorophyll a with standard error of the mean from triplicates. (B) Silicate with standard error of the mean from duplicates. (C) Phosphate with standard error of the mean from duplicates. (D) Nitrate+ nitrite with standard error of the mean from duplicates. (E) Temperature with each point as one GO-FLO bottle (SOG samples) or from total seawater sample (Jericho samples). (F) Salinity with each point representing a seawater sample as one GO-FLO bottle (SOG samples) or from total seawater sample (Jericho samples).

Figure 3

Rarefaction curves. Rarefaction analysis of RdRp amplicons based on Chao1 richness analysis of operational taxonomic units (OTUs) at 95% similarity. Rarefaction curves were resampled using number of reads recovered per library. Rarefaction curves plateau indicating adequate sequencing for these samples.

Figure 4

Euler diagrams of normalized RdRp OTUs. (A) Euler diagram of Jericho Pier samples. (B) Euler diagram of SOG samples. The OTUs presented were from reads clustered at 95% similarity, comprise only OTUs that could be aligned to the NCBI CDD RdRp alignment, and contained the RdRp motif C. The diagrams were constructed using the venneuler() algorithm (Wilkinson, 2011). The size of the circles is approximately proportional to the number of OTUs recovered per site. The overlap in the diagram describes OTUs that were found at multiple sites and the non-overlapping areas describe OTUs that were unique to that site.

Figure 5

Rank abundance by site. Relative abundance of OTUs in each sample ordered by rank abundance: (A) Jericho Summer, (B) Jericho Fall, (C) SOG Station 1, (D) SOG Station 2, (E) SOG Station 4. OTUs were clustered at 95% amino acid similarity and OTU relative abundances were normalized to the sample with the lowest number of reads.

Figure 6

Phylogenetic tree with heatmap. Maximum likelihood (RA×ML) tree of RdRp OTUs that contained more than 5 reads and relevant Picornavirales sequences. Bootstrap values above 65% are labeled. Adjacent to the tips of the tree is a heatmap displaying the relative abundance of each OTU at 95% similarity by site. OTU relative abundances were normalized to the sample with the lowest number of reads.